## [1] "O76_p4_IFNg_R1_2.hicup.bam"

Truncation & Mapping

Truncation Frequency

Category Read 1 Read 2
Total 64,133,961 64,133,961
Not Truncated 39,030,916 39,002,865
Truncated 25,103,045 25,131,096

Truncated Read Length

Category Read 1 Read 2
Average Length Truncated 47.6 45.5

Mapping Efficiency

Category Read 1 Read 2
Too Short To Map 3,949,166 4,046,436
Unique Alignments 55,068,279 54,066,564
Multiple Alignments 2,288,807 1,997,064
Failed To Align 2,827,709 4,023,897
Paired 47,066,050 47,066,050

Truncation and Mapping Bar Plot

Filtering

Filtering Breakdown by Category

Category Count
Valid Pairs 26,549,206
Invalid Pairs 20,516,844
Same Circularised 584,200
Same Dangling Ends 3,759,715
Same Fragment Internal 9,041,643
Re Ligation 5,290,816
Contiguous Sequence 111,049
Wrong Size 1,729,421
Total Pairs 47,066,050

Filtering Breakdown Pie Chart

Ditag Length Distribution

Frequency Line Plot

Deduplication

Deduplication Summary Table

Category All Ditags Unique Ditags
Read Pairs 26,549,206 38,541
Cis-close (<10Kbp) 3,446,749 4,190
Cis-far (>10Kbp) 15,839,281 21,264
Trans 7,263,176 13,087

Deduplication Bar Chart

Analysis produced by HiCUP - a tool for mapping and performing quality control on Hi-C data

Babraham Bioinformatics